Re: [R] Calculating Goodman-Kurskal's gamma using delta method

code... Could anyone point out what the problem is? Thanks. Wuming Save your time (and much execution time) by using the Hmisc package's rcorr.cens function with the argument outx=TRUE. rcorr.cens using a standard U-statistic variance estimator. -- Frank E Harrell Jr Professor

Re: [R] C-index : typical values

of C-index. Thank you very much in advance. Regards, Adai __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell

Re: [R] p-value in lrm

nonlinear effects, interactions, etc. If by get you mean retrieve for use in other code you can look at print.lrm for hints, or use coef(fit) and diag(Varcov(fit)). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] staying with R, jobs in R

The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] stratified Wilcoxon available?

of such a stratified test as part of a proportional odds model with adjustment for strata as main effects. The Wilcoxon tests is a special case of the PO model. You can fit it with polr or lrm. -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] survival parametric question

]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] compare c-index of two logistic models using rcorrp.senc() of the Hmisc library

method, within paired predictions. You can't get a difference in ROC areas from the U-statistic computed by rcorrp.cens. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] translating output ( latex()....)

that Brian Ripley mentioned) and wanted to use that to enhance print. and latex. methods for the summary.formula family of functions, and know or can learn how to use CVS, we will consider giving you access to the Hmisc CVS repository to make the enhancements you want. Frank -- Frank E Harrell

Re: [R] How to add legend of plot.Design function (method=image)? (if (!.R.) )

-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] Penalized likelihood-ratio chi-squared statistic: L.R. model for Goodness of fit?

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Concerning reading of SAS-files

bogdan romocea wrote: The first one is an index, not a data set. Anyway, just use SAS to export the data sets in text format (CSV, tab-delimited etc). You can then easily read those in R. (By the way, the help for read.xport says that 'The file must be in SAS XPORT format.' Is .sas7bdat an

Re: [R] connexion problem getHdata (HMisc)

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Hmisc / Design question

, df)) ## What is alpha if using T-statistic ? return(list(w.alpha=w.alpha, alpha.star=alpha.star)) } -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Help with sas.get

guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https

Re: [R] Binary outcome with non-absorbing outcome state

]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] CSV file and date. Dates are read as factors!

] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics

Re: [R] conversion from SAS

-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] Displaying p-values in latex

-value printing as requested. Look at anova.Design for the code. -Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch

Re: [R] cor(X) with P-Value

$P 0.001080 CT23$V 0.2643529 But I do not know how. cheers Worik library(Hmisc) rcorr(cbind(. . . .)) -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] aregImpute in Hmisc

with that many variables. -Frank Harrell __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair

Re: [R] ROC curve with survival data

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Survival dummy variables and some questions

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] Survival dummy variables and some questions

by constructing something on the right hand side of the model. But if you have a simple historical covariate such as previous history of disease before the start of follow-up time that's ok. Frank Original Message - From: Frank E Harrell Jr To: Stephen Cc: Sent: Monday, July 18, 2005 2:46 PM

Re: [R] Survival dummy variables and some questions

don't require categorization. You can request predicted values at any sequence of ages. If you want hazard ratios you can take differences in predicted log hazards and antilog them. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] read.xport

/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] read.xport

with sasxport.get that reads csv files. The help file has a URL with a full howto. Frank Thanks. -Original Message- From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED] Sent: Thursday, July 14, 2005 11:46 AM To: bogdan romocea Cc: Nelson, Gary (FWE); R-help@stat.math.ethz.ch Subject: Re: [R

Re: [R] Design: predict.lrm does not recognise lrm.fit object

-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] Calculation of group summaries

] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] validation, calibration and Design

the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list

Re: [R] aregImpute: beginner's question

, : inconsistant naming of observations led to differing length vectors -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch

Re: [R] missing data imputation

distribution. so that the Rubin/Shafer method described above (see paragraph about dispersion of imputed values) is not fully implemented. Best wishes, Ted. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics

Re: [R] removing factor level represented by less than x rows

be a fairly common task with a straight forward solution that I can't see. Any ideas? Best wishes, Mikkel library(Hmisc) ?combine.levels This doesn't remove levels but combines infrequent ones though. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] missing data imputation

- prelim.norm(tc) thetahat - em.norm(s) #find the MLE for a starting value theta - da.norm(s,thetahat,steps=20,showits=TRUE,return.ymis=TRUE) #take 20 steps ximp - imp.norm(s,thetahat,tc) #impute missing data under the MLE -- Frank E Harrell Jr Professor and Chair School

Re: [R] mApply instead of by ???

Marten Winter wrote: Now that's a brief note. mApply in the Hmisc package may have large speed advantages over by for large datasets. Also look at the summarize function in Hmisc, which uses mApply. -- Frank E Harrell Jr Professor and Chair School of Medicine

[R] Possible bug in summary of residuals with lm and weights

0.89438636 version platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor1.0 year 2005 month04 day 18 language R -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] delta-beta's

/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] R demos

, Federico Calboli -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] Representative curves

Can someone point me to R code or recent publications dealing with selection of representative time-response profiles in longitudinal data from datasets containing a large number of subject's profiles? Thanks Frank -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] How to use expression in label with xYplot

do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch

Re: [R] analyzing suvival data using splines (a.k.a., piecewise log-hazard-ratio models)

/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] questions on bootstrap

at documentation for ols and validate.ols. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] ordinary polynomial coefficients from orthogonal polynomials?

mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] ordinary polynomial coefficients from orthogonal polynomials?

Prof Brian Ripley wrote: On Tue, 14 Jun 2005, Frank E Harrell Jr wrote: Prof Brian Ripley wrote: On Tue, 14 Jun 2005, James Salsman wrote: How can ordinary polynomial coefficients be calculated from an orthogonal polynomial fit? Why would you want to do that? predict() is perfectly

Re: [R] position of a legend-object

for your help. Carsten There are functions in the Hmisc package to help too (especially labcurve and xYplot). You can have a function put a legend in the most empty portion of a graph automatically with these functions. -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] sapply following using by with a list of factors

have not quite got this right...can you help? Thanks in advance Sam Sam McClatchie, Biological oceanography South Australian Aquatic Sciences Centre You might try the summarize function in the Hmisc package. -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] Power set

a single model :-) Frank Harrell Anyhow, is there a function to produce the right hand side of the formulas, please? thanks, Laura Holt mailto: [EMAIL PROTECTED] R Version 2.1.0 Windows -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] obtaining first and last record for rows with same identifier

might also look at section 4.3 of http://biostat.mc.vanderbilt.edu/twiki/pub/Main/RS/sintro.pdf -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] Hmisc/Design and problem with cgroup

Uwe Ligges wrote: Aric Gregson wrote: On 5/17/05 21:44 Frank E Harrell Jr sent the following: Aric Gregson wrote: Hello, I am trying to use the following to output a table to latex: cohortbyagesummary - by(data.frame(age,ethnicity), cohort, summary) w - latex.default(cohortbyagesummary

Re: [R] logistic regression: differential importance of regressors

. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Conflict between xtable and Hmisc when using Sweave?

problem because Hmisc has being using label and label- since 1991. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing

Re: [R] inserting R code in a latex document

, and am changing - to left arrows and ~ to $\sim$. This also requires the LaTeX relsize package. Thanks -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] Standardized logistic regression coefficients

coefficients? Thanks in advance! Alexander Roth Design doesn't implement those because they have terrible properties. Instead consider interquartile-range odds ratios (done by summary.Design by typing summary(. . .)). -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] Does R have a command for sending emails?

(cmd) -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] help for bootstrap of backward stepwise logistic regression

, calibrate.lrm Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] Step wise regression

predictors) x[,sample(ncol(x))] :-) -Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] Step wise regression

(Ted Harding) wrote: On 03-May-05 Frank E Harrell Jr wrote: walmir-rodrigues wrote: Dear Fellows, How can I do to proced a step wise regression in R, if it´s possible ? Thanks, Walmir Here is an easy approach that will yield results only slightly less valid than one actually using the response

Re: [R] Restricted cubic spline function ERROR?: glm(Y~rcs(x,5))

don't), Design wants you to use glmD. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] normality test

, and an assumption of high power for the tests (qq plots don't always help with that because of their subjectivity). When possible it's good to choose a robust method. Also, doing pre-testing for normality can affect the type I error of the overall analysis. -- Frank E Harrell Jr Professor and Chair

Re: [R] normality test

, IL 61820 On Apr 28, 2005, at 7:46 AM, Frank E Harrell Jr wrote: Usually (but not always) doing tests of normality reflect a lack of understanding of the power of rank tests, and an assumption of high power for the tests (qq plots don't always help with that because of their subjectivity). When

Re: [R] How to break data in quantiles properly?

=matrix(0,1000,1) x[100]=1 Classify.Quantile(x, 10) of course this dataset is a bit extreme but it happens to get data with very small variance. Thanks for any help you could provide The cut2 function in the Hmisc package may help. -FH -- Frank E Harrell Jr Professor and Chair School

Re: [R] missing values

like exactly what aregImput() is good for, or transcan(), depending on whether you need to make inferences (and hence do multiple imputation). Jon For those interested I have preprints of a paper comparing MICE, aregImpute, and transcan on the basis of simulations. -- Frank E Harrell Jr

Re: Re : Thanks! (Was: Re: [R] R-2.1.0 is released)

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R

Re: [R] Re: HOWTO compare univariate binomial glm lrm models which are not nested

272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list

Re: [R] Re: HOWTO compare univariate binomial glm lrm models which are not nested

-chosen models or you will invalidate inference and estimates if you use these comparisons to build a final model. Frank *** -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Range in probabilities of a fitted lrm model (Y~X)

Tel: +32-16-329750 Fax: +32-16-329760 http://gloveg.kuleuven.ac.be/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell

Re: [R] How to calculate the AUC in R

. Unfortunately I don't know how to calculate the AUC. Someone can point me an example of this procedure or a package that implements this calculation? Thanks for the help, João Paulo Dubas. One of many ways: trap.rule - function(x,y) sum(diff(x)*(y[-1]+y[-length(y)]))/2 -- Frank E Harrell Jr Professor

Re: [R] exclusion rules for propensity score matchng (pattern rec)

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] exclusion rules for propensity score matchng (pattern rec)

. Frank Harrell On Tue, 5 Apr 2005, Frank E Harrell Jr wrote: [EMAIL PROTECTED] wrote: Dear R-list, i have 6 different sets of samples. Each sample has about 5000 observations, with each observation comprised of 150 baseline covariates (X), 125 of which are dichotomous. Roughly 20

[R] (no answer)

I wish to perform brain surgery this afternoon at 4pm and don't know where to start. My background is the history of great statistician sports legends but I am willing to learn. I know there are courses and numerous books on brain surgery but I don't have the time for those. Please direct me

Re: [R] question

Baarle [EMAIL PROTECTED] You didn't say which prostate cancer study that represented. One famous one has data in R form on our web site http://biostat.mc.vanderbilt.edu. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics

Re: [R] fastbw question

www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E

Re: [R] R-squared in Logistic Regression

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Confidence interval for Tau-a or c-index to compare logistic lrm (binary) models with each other.

do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing

Re: [R] Logistic regression goodness of fit tests

Trevor Wiens wrote: On Thu, 10 Mar 2005 16:19:41 -0600 Frank E Harrell Jr [EMAIL PROTECTED] wrote: The goodness of fit test only works on prespecified models. It is not valid when stepwise variable selection is used (unless perhaps you use alpha=0.5). Perhaps I'm blind, but I can't find any

Re: [R] Logistic regression goodness of fit tests

on prespecified models. It is not valid when stepwise variable selection is used (unless perhaps you use alpha=0.5). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

[R] Quantian

Congratulations Dirk on the article in linuxtoday.com today about Quantian. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch

Re: [R] subset selection for logistic regression

linear models (particularly the fitting of logistic relationships), the complexity is greatly increased. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] subset selection for logistic regression

. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] subset selection for logistic regression

PROTECTED] On Behalf Of Frank E Harrell Jr Sent: Wednesday, March 02, 2005 5:13 AM To: Wittner, Ben Cc: [EMAIL PROTECTED] Subject: Re: [R] subset selection for logistic regression Wittner, Ben wrote: R-packages leaps and subselect implement various methods of selecting best or good subsets

Re: [R] Teaching R in 40 minutes. What should be included?

(manuals, FAQ, community) as a starter to learn, use and program R by themselves. I think this would do for a 40 minutes presentation without taking the risk to deter people due to overcomplexity. regards Thomas -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] Forward Stepwise regression based on partial F test

accuracy and that violates every aspect of statistical inference, you are on the right track. See http://www.stata.com/support/faqs/stat/stepwise.html for details. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] Re:logistic regression

. . -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Re:logistic regression

at the Bioconductor website. There was also some code sent around on the list a few months back for calculating trapeziodal AUC, se's from ROC, and comparing two ROC curves...search the archives if interested, or I can probably dig them out for you offline... Cheers, Joe Quoting Frank E Harrell Jr [EMAIL

Re: [R] Programming/scripting with expressions - variables

not need to create new variables at all. Franc -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] no. at risk in survfit()

get them? Thanks The Design package's survplot function can print n.risk over equally spaced time points. You might see an easy way to print this by looking at the code. -Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] logistic regression 3D-plot

=NA, fun='plogis') # probability scale -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] logistic regression 3D-plot CORRECTION

library(Design) d - datadist(mydata); options(datadist='d') f - lrm(incidence ~ sun*trees) # lrm is for binary or ordinal response plot(f, sun=NA, trees=NA) # add method='image' or 'contour' to get other types of graphs plot(f, sun=NA, trees=NA, fun='plogis') # probability scale Correction:

Re: [R] Reading Dates in a csv File

do not know and have not figured out how to do that. Any suggestion(s) would be greatly appreciated. Thanks, Charles The csv.get function in the Hmisc package may do most of what you want. -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] (no subject)

(parametric model) ? Thanks Virginie In the Design package look at the pphsm function that converts a survreg Weibull fit (fitted by the psm function which is an adaptation of survreg) to PH form. -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] Cross-validation accuracy in SVM

mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Omitting constant in ols() from Design

can't use lm(), because robcov() needs an object from the Design() series. Or is there a different way to go about this? Tobias Muhlhofer ols does not support this. Sorry. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics

Re: [R] bwplot: how not to draw outliers

the scale), you will have to modify the panel.bwplot function in addition to using the above. --sundar You may also want to try library(Hmisc) library(lattice) bwplot(..., panel=panel.bpplot) ?panel.bpplot -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] empirical (sandwich) SE estimate in lme ()?

-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help

Re: [R] Standard error for the area under a smoothed ROC curve?

in Wilcoxon. As Somers' Dxy rank correlation coefficient is 2*(1-C) where C is the concordance or ROC area, the Hmisc package function rcorr.cens uses U statistic methods to get the standard error of Dxy. You can easily translate this to a standard error of C. Frank -- Frank E Harrell Jr

Re: [R] transcan() from Hmisc package for imputing data

frame with the NA values filled up? Or is there any other function that i could use? Thank you avneet It's in the help file for transcan. But multiple imputation is much better, and transcan does not do multiple imputation as well as the newer Hmisc function aregImpute. -- Frank E Harrell Jr

Re: [R] Kolmogorov-Smirnof test for lognormal distribution with estimated parameters

. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Standard error for the area under a smoothed ROC curve?

Dan Bolser wrote: On Wed, 12 Jan 2005, Frank E Harrell Jr wrote: Dan Bolser wrote: Hello, I am making some use of ROC curve analysis. I find much help on the mailing list, and I have used the Area Under the Curve (AUC) functions from the ROC function in the bioconductor project... http

Re: [R] R-etiquette

to include their names in an Ack. section, usually. Referencing as a personal communication is perhaps better. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] R-etiquette

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] R-etiquette

Prof Brian Ripley wrote: On Sun, 9 Jan 2005, Anne wrote: I'm about to present a report (for internal use of governmental agency). I used extensively R , contibuted packages, as well as communications on the R-list As well as citing R, I would like to know how to cite the contributed packages

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